The Department of Conservation and Oceana Gold have reached an agreement on a proposed expansion at Macrae's mine in East Otago.
The mine is on private land. The area is also home to rare native plant and animal species.
The agreement will result in Oceana Gold signing convenants that will permanently protect 155 hectares of comparable habitat.
The company will fund a $100,000 programme to maintain populations of the roundhead Galaxias, an acutely threatened fish.
In turn, DoC will not oppose applications for the mine's expansion.